Compare revisions

Johannes Hjorth · Eleni Mathioulaki · Eleni Mathioulaki · Eleni Mathioulaki · Abolfazl Ziaeemehr · Eleni Mathioulaki
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -4,10 +4,12 @@ stages:

 variables:
  BUILD_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/ebrains-spack-build-env/base:devel
+  RUN_ENV_DOCKER_IMAGE: docker-registry.ebrains.eu/clb-jupyter-image/ebrains:dev-a7ab31be
  SPACK_PATH_GITLAB: /mnt/spack_v0.23.1
  SYSTEMNAME: ebrainslab
  GIT_SUBMODULE_STRATEGY: recursive
  GIT_CLEAN_FLAGS: -ffdxq
+  RUNNER_AFTER_SCRIPT_TIMEOUT: 20m

 # ===================================================================
 # LAB DEPLOYMENTS
@@ -47,6 +49,15 @@ variables:
    - if [ $(kubectl get pods -l job-name=simplejob${CI_PIPELINE_ID} -o jsonpath='{.items[0].status.containerStatuses[0].state.terminated.exitCode}') -ne 0 ]; then exit 1; fi;
    # delete the job, as we have the logs here
    - kubectl delete job simplejob${CI_PIPELINE_ID} || true
+  after_script:
+    - kubectl config use-context $KUBE_CONTEXT
+    - sh create_job_widget_script.sh $CI_PIPELINE_ID $RUN_ENV_DOCKER_IMAGE $INSTALLATION_ROOT $SPACK_ENV $RELEASE_NAME $LAB_KERNEL_ROOT
+    - cat widget-script.yml
+    - kubectl create -f widget-script.yml
+    - while true; do sleep 300; x=$(kubectl get pods -l job-name=widget-script${CI_PIPELINE_ID} -o jsonpath='{.items[0].status.phase}'); if [ $x != "Running" ]; then break; fi; done
+    - kubectl logs jobs/widget-script${CI_PIPELINE_ID} | tee log.txt
+    - if [ $(kubectl get pods -l job-name=widget-script${CI_PIPELINE_ID} -o jsonpath='{.items[0].status.containerStatuses[0].state.terminated.exitCode}') -ne 0 ]; then exit 1; fi;
+    - kubectl delete job widget-script${CI_PIPELINE_ID} || true
  # artifacts:
  #   paths:
  #     - spack_logs
@@ -97,12 +108,24 @@ variables:
 # -------------------------------------------------------------------

 # deploy int release (latest changes) to dev env to be tested before release to production
+# (the master branch and any branch starting with "lab-" is deployed to a dedicated kernel)
 .deploy-int-release:
  variables:
-    SPACK_ENV: test
-    RELEASE_NAME: EBRAINS-test
+    SPACK_ENV: $CI_COMMIT_BRANCH
+    RELEASE_NAME: $CI_COMMIT_BRANCH
  rules:
-    - if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE == "push"
+    - if: '($CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH || $CI_COMMIT_BRANCH =~ /^lab-/) && $CI_PROJECT_NAMESPACE =~ /platform\/esd/ && $CI_PIPELINE_SOURCE == "push"'
+
+# deploy a pre-production environment first, to avoid directly modifying the experimental or official release environments
+.deploy-ppd-release:
+  variables:
+    SPACK_ENV: ppd
+    RELEASE_NAME: EBRAINS-ppd
+  allow_failure: false
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "schedule"  && $DEPLOYMENT == "prod"
+    - if: $CI_COMMIT_BRANCH =~ /^ebrains/
+      when: manual

 # deploy the experimental release of tools once a week from latest working version of int release 
 .deploy-exp-release:
@@ -125,8 +148,8 @@ variables:
 # deploy the production release of tools
 .deploy-prod-release:
  variables:
-    SPACK_ENV: ebrains-24-04
-    RELEASE_NAME: EBRAINS-24.04
+    SPACK_ENV: ebrains-25-02
+    RELEASE_NAME: EBRAINS-25.02
  rules:
    - if: $CI_COMMIT_BRANCH =~ /^ebrains/
      when: manual
@@ -147,26 +170,42 @@ deploy-exp-release-dev-cineca:
    - .deploy-exp-dev-release
    - .deploy-dev-server-cineca

+# deploy ppd release to prod environment at JSC
+deploy-ppd-release-prod-jsc:
+  extends:
+    - .deploy-ppd-release
+    - .deploy-prod-server-jsc
+
+# deploy ppd release to prod environment at CINECA
+deploy-ppd-release-prod-cineca:
+  extends:
+    - .deploy-ppd-release
+    - .deploy-prod-server-cineca
+
 # deploy exp release to prod environment at JSC
 deploy-exp-release-prod-jsc:
+  needs: [deploy-ppd-release-prod-jsc]
  extends:
    - .deploy-exp-prod-release
    - .deploy-prod-server-jsc

 # deploy exp release to prod environment at CINECA
 deploy-exp-release-prod-cineca:
+  needs: [deploy-ppd-release-prod-cineca]
  extends:
    - .deploy-exp-prod-release
    - .deploy-prod-server-cineca

 # deploy prod release to prod environment at JSC
 deploy-prod-release-prod-jsc:
+  needs: [deploy-ppd-release-prod-jsc]
  extends:
    - .deploy-prod-release
    - .deploy-prod-server-jsc

 # deploy prod release to prod environment at CINECA
 deploy-prod-release-prod-cineca:
+  needs: [deploy-ppd-release-prod-cineca]
  extends:
    - .deploy-prod-release
    - .deploy-prod-server-cineca

--- a/create_JupyterLab_kernel.sh
+++ b/create_JupyterLab_kernel.sh
@@ -37,7 +37,7 @@ cp $INSTALLATION_ROOT/spack/var/spack/environments/$EBRAINS_SPACK_ENV/load_env.s
 # and the location of python modules installed in the base docker Collab image
 cat <<EOF >> $KERNEL_PATH/bin/env.sh
 export PATH=\$PATH:/opt/app-root/src/.local/bin
-export PYTHONPATH=\$PYTHONPATH:/opt/app-root/src/.local/lib/python3.8/site-packages:/usr/local/lib/python3.8/dist-packages
+export PYTHONPATH=\$PYTHONPATH:/opt/conda/lib/python3.11/site-packages
 export R_LIBS_USER=/opt/app-root/src/.local/lib/R/site-library
 mkdir -p \$R_LIBS_USER
 export R_LIBS=\$R_LIBS_USER:\$R_LIBS

--- a/create_job.sh
+++ b/create_job.sh
@@ -105,13 +105,6 @@ spec:
          persistentVolumeClaim:
            claimName: shared-binaries
        - name: tmp
-          ephemeral:
-            volumeClaimTemplate:
-              spec:
-                accessModes: [ "ReadWriteMany" ]
-                storageClassName: "longhorn-0"
-                resources:
-                  requests:
-                    storage: 50Gi
+          emptyDir: {}
      restartPolicy: Never
 EOT
--- a/create_job_widget_script.sh
+++ b/create_job_widget_script.sh
+#!/bin/bash
+
+# ===========================================================================================================
+# title         : create_job_widget_script.sh
+# usage         : ./create_job_widget_script.sh $OC_JOB_ID $RUN_ENV_DOCKER_IMAGE $INSTALLATION_ROOT
+#                 $SPACK_ENV $RELEASE_NAME $LAB_KERNEL_ROOT
+# description   : creates job file that generates a script to load the jupyter extensions for a given env
+# ===========================================================================================================
+
+OC_JOB_ID=$1
+RUN_ENV_DOCKER_IMAGE=$2
+INSTALLATION_ROOT=$3
+EBRAINS_SPACK_ENV=$4
+RELEASE_NAME=$5
+LAB_KERNEL_ROOT=$6
+
+cat <<EOT >> widget-script.yml
+apiVersion: batch/v1
+kind: Job
+metadata:
+  name: widget-script${OC_JOB_ID}
+spec:
+  parallelism: 1
+  completions: 1
+  backoffLimit: 0
+  template:
+    spec:
+      containers:
+      - name: widget-script
+        image: ${RUN_ENV_DOCKER_IMAGE}
+        imagePullPolicy: Always
+        resources:
+          limits:
+            cpu: '1'
+            memory: '1Gi'
+          requests:
+            cpu: '0.5'
+            memory: '500Mi'
+        volumeMounts:
+          - name: sharedbin
+            mountPath: /srv
+        command:
+        - /bin/bash
+        - -c
+        - |
+          . \$INSTALLATION_ROOT/spack/share/spack/setup-env.sh
+          spack env activate --without-view \$EBRAINS_SPACK_ENV
+          KERNEL_PATH=\$LAB_KERNEL_ROOT/\$(echo "\$RELEASE_NAME" | tr '[:upper:]' '[:lower:]')
+          spack load --sh --first clb-nb-utils py-pip py-tvb-ext-bucket py-tvb-ext-unicore py-tvb-ext-xircuits > \$KERNEL_PATH/bin/widget_activation.sh
+        env:
+          - name: SYSTEMNAME
+            value: ebrainslab
+          - name: SPACK_DISABLE_LOCAL_CONFIG
+            value: "true"
+          - name: INSTALLATION_ROOT
+            value: "$INSTALLATION_ROOT"
+          - name: EBRAINS_SPACK_ENV
+            value: "$EBRAINS_SPACK_ENV"
+          - name: RELEASE_NAME
+            value: "$RELEASE_NAME"
+          - name: LAB_KERNEL_ROOT
+            value: "$LAB_KERNEL_ROOT"
+      volumes:
+        - name: sharedbin
+          persistentVolumeClaim:
+            claimName: shared-binaries
+      restartPolicy: Never
+EOT
--- a/install_spack_env.sh
+++ b/install_spack_env.sh
@@ -96,9 +96,6 @@ cp /tmp/spack.yaml ${CI_SPACK_ROOT}/var/spack/environments/$EBRAINS_SPACK_ENV/
 # activate environment
 spack env activate --without-view $EBRAINS_SPACK_ENV

-# deactivate view during concretization and installation
-spack env view disable
-
 spack concretize --force --fresh --test root

 # dump dag to file
@@ -133,9 +130,9 @@ spack-python -c "exit(not len(spack.environment.active_environment().uninstalled
    else
        echo "Updating of the source cache disabled."
    fi
-    if [ "$ret" -ne 0 ]; then
-        (exit $ret)
-    fi
+    # if [ "$ret" -ne 0 ]; then
+    #     (exit $ret)
+    # fi
 )

 if [ -n "${OCI_CACHE_PREFIX}" ]; then
@@ -147,10 +144,6 @@ fi
 # delay exit code until we have updated the cache below
 spack install --no-check-signature -y -j$SPACK_JOBS --fresh --test root && spack_install_ret=$? || spack_install_ret=$?

-# re-enable view
-spack env view enable
-spack env view regenerate
-
 # no need to update the local cache nor the remote cache if we don't want to update
 if [ -n "${OCI_CACHE_PREFIX}" ] && [ "${UPDATE_SPACK_OCI_CACHES:-false}" = "true" ]; then
    # push previously missing (but now installed) packages to the local cache

--- a/packages/cudnn/package.py
+++ b/packages/cudnn/package.py
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+import os
+import platform
+
+from spack.package import *
+
+_versions = {
+    # cuDNN 9.8.0
+    "9.8.0.87-12": {
+        "Linux-x86_64": "321b9b33bb1287404d93d5672d352f16feabc4b220ac6ae0b86e4b27f257dcf4",
+        "Linux-aarch64": "f03ece3ff07d1719f06218973a8797cec1be387cc317baab5bb118dc988199e7",
+    },
+    "9.8.0.87-11": {
+        "Linux-x86_64": "cf4dfaef8311d987d640a322f668cd5240ac3e5302abe9617dd991b5b2532758"
+    },
+    # cuDNN 9.2.0
+    "9.2.0.82-12": {
+        "Linux-x86_64": "1362b4d437e37e92c9814c3b4065db5106c2e03268e22275a5869e968cee7aa8",
+        "Linux-aarch64": "24cc2a0308dfe412c02c7d41d4b07ec12dacb021ebf8c719de38eb77d22f68c1",
+    },
+    "9.2.0.82-11": {
+        "Linux-x86_64": "99dcb3fa2bf7eed7f35b0f8e58e7d1f04d9a52e01e382efc1de16fed230d3b26"
+    },
+    # cuDNN 8.9.7
+    "8.9.7.29-12": {
+        "Linux-x86_64": "475333625c7e42a7af3ca0b2f7506a106e30c93b1aa0081cd9c13efb6e21e3bb",
+        "Linux-ppc64le": "8574d291b299f9cc0134304473c9933bd098cc717e8d0876f4aba9f9eebe1b76",
+    },
+    "8.9.7.29-11": {
+        "Linux-x86_64": "a3e2509028cecda0117ce5a0f42106346e82e86d390f4bb9475afc976c77402e",
+        "Linux-ppc64le": "f23fd7d59f9d4f743fa926f317dab0d37f6ea21edb2726ceb607bea45b0f9f36",
+    },
+    # cuDNN 8.9.5
+    "8.9.5.30-12": {
+        "Linux-x86_64": "2a2eb89a2ab51071151c6082f1e816c702167a711a9372f9f73a7b5c4b06e01a",
+        "Linux-ppc64le": "38388ec3c99c6646aaf5c707985cd35e25c67f653d780c4081c2df5557ab665f",
+        "Linux-aarch64": "0491f7b02f55c22077eb678bf314c1f917524bd507cf5b658239bf98a47233a1",
+    },
+    "8.9.5.30-11": {
+        "Linux-x86_64": "bbe10e3c08cd7e4aea1012213781e4fe270e1c908263444f567cafefb2cc6525",
+        "Linux-ppc64le": "d678f8b2903b95de7eeaef38890c5674705864ea049b2b63e90565f2c0ea682f",
+    },
+    # cuDNN 8.9.0
+    "8.9.0.131-12": {
+        "Linux-x86_64": "477631002be61022b60961cba0a501271507a93f81d6b08384bc320cb8706c98",
+        "Linux-ppc64le": "ff239e4cbbf21fa18104b62a887686e2197f820ad58817d62e509c735a331829",
+        "Linux-aarch64": "fab70f4fb3b933ff502200a1d954d2c6fc205ff9c9b1d271ea4c41e980a66596",
+    },
+    "8.9.0.131-11": {
+        "Linux-x86_64": "3cb82c50723f14b41d43523f222cd52cc9d50b3ad67c380f4be51bd1133daa2d",
+        "Linux-ppc64le": "18778de490550c5b584e96560208e5e37678397037946e10a1c2824174c69725",
+    },
+    # cuDNN 8.8.1
+    "8.8.1.3-12": {
+        "Linux-x86_64": "79d77a769c7e7175abc7b5c2ed5c494148c0618a864138722c887f95c623777c",
+        "Linux-ppc64le": "b0e89021a846952cad8cfc674edce2883f6e344ebd47a2394f706b1136715bc7",
+    },
+    "8.8.1.3-11": {
+        "Linux-x86_64": "af7584cae0cc5524b5913ef08c29ba6154113c60eb0a37a0590a91b515a8a8f9",
+        "Linux-ppc64le": "d086003d09d5388aa42142f07483a773aa74b602478b0933e24fc63f56f1658f",
+    },
+    # cuDNN 8.7.0
+    "8.7.0.84-11.8": {
+        "Linux-x86_64": "976c4cba7233c97ae74006afab5172976300ba40f5b250a21f8cf71f59c9f76d",
+        "Linux-ppc64le": "0433d6d8b6841298e049e8a542750aa330a6e046a52ad95fae0c2f75dabe5575",
+        "Linux-aarch64": "cf967f78dbf6c075243cc83aa18759e370db3754aa15b12a0a14e8bf67a3a9d4",
+    },
+    # cuDNN 8.6.0
+    "8.6.0.163-11.8": {
+        "Linux-x86_64": "bbc396df47294c657edc09c600674d608cb1bfc80b82dcf4547060c21711159e",
+        "Linux-ppc64le": "c8a25e7e3df1bb9c4e18a4f24dd5f25cfd4bbe8b7054e34008e53b2be4f58a80",
+        "Linux-aarch64": "a0202278d3cbd4f3adc3f7816bff6071621cb042b0903698b477acac8928ac06",
+    },
+    # cuDNN 8.5.0
+    "8.5.0.96-11.7": {
+        "Linux-x86_64": "5454a6fd94f008728caae9adad993c4e85ef36302e26bce43bea7d458a5e7b6d",
+        "Linux-ppc64le": "00373c3d5e0b536a5557d0d0eb50706777f213a222b4030e1b71b1bec43d205f",
+        "Linux-aarch64": "86780abbecd4634e7363fad1d000ae23b7905a5f8383bddbf7332c6934791dde",
+    },
+    # cuDNN 8.4.0
+    "8.4.0.27-11.6": {
+        "Linux-x86_64": "d19bdafd9800c79d29e6f6fffa9f9e2c10d1132d6c2ff10b1593e057e74dd050",
+        "Linux-ppc64le": "7ef72353331cf42b357f53cb4a4971fb07e2f0b2ae66e03d54933df52de411c8",
+        "Linux-aarch64": "3972ab37b6f0271274931f69c5675c3b61d16f8f5a2dedd422a5efd7b0f358e5",
+    },
+    "8.4.0.27-10.2": {
+        "Linux-x86_64": "14c5e3ca4258271996d1fd959c42d17c582ce4d9aff451f84524469e784fd154"
+    },
+    # cuDNN 8.3.3
+    "8.3.3.40-11.5": {
+        "Linux-x86_64": "eabe96c75cf03ea4f5379894d914f1f8ae14ceab121989e84b0836d927fb7731",
+        "Linux-ppc64le": "eaedc8dea675767f9445c11d96e6b472110d2fed728db4179153ca7da6503083",
+        "Linux-aarch64": "83b1d21b0f6495dfdc2316e6d53489db8ab1b752e4e4d21caca0a08fb2136cdc",
+    },
+    "8.3.3.40-10.2": {
+        "Linux-x86_64": "d8554f2b32e6295d5fc8f3ac25e68f94058b018c801dab9c143e36812f8926ab"
+    },
+    # cuDNN 8.3.2
+    "8.3.2.44-11.5": {
+        "Linux-x86_64": "5500953c08c5e5d1dddcfda234f9efbddcdbe43a53b26dc0a82c723fa170c457",
+        "Linux-ppc64le": "0581bce48023a3ee71c3a819aaefcabe693eca18b61e2521dc5f8e6e71567b1b",
+        "Linux-aarch64": "7eb8c96bfeec98e8aa7cea1e95633d2a9481fc99040eb0311d31bf137a7aa6ea",
+    },
+    # cuDNN 8.3.1
+    "8.3.1.22-11.5": {
+        "Linux-x86_64": "f5ff3c69b6a8a9454289b42eca1dd41c3527f70fcf49428eb80502bcf6b02f6e",
+        "Linux-ppc64le": "1d2419a20ee193dc6a3a0ba87e79f408286d3d317c9831cbc1f0b7a268c100b0",
+        "Linux-aarch64": "ff23a881366c0ee79b973a8921c6dd400628a321557550ad4e0a26a21caad263",
+    },
+    # cuDNN 8.2.4
+    "8.2.4.15-11.4": {
+        "Linux-x86_64": "0e5d2df890b9967efa6619da421310d97323565a79f05a1a8cb9b7165baad0d7",
+        "Linux-ppc64le": "af8749ca83fd6bba117c8bee31b787b7f204946e864294030ee0091eb7d3577e",
+        "Linux-aarch64": "48b11f19e9cd3414ec3c6c357ad228aebbd43282aae372d42cab2af67c32a08b",
+    },
+    # cuDNN 8.2.0
+    "8.2.0.53-11.3": {
+        "Linux-x86_64": "7a195dc93a7cda2bdd4d9b73958d259c784be422cd941a9a625aab75309f19dc",
+        "Linux-ppc64le": "cfe06735671a41a5e25fc7542d740177ac8eab1ab146bd30f19e0fa836895611",
+        "Linux-aarch64": "0f44af94eef7826dc7b41f92aade3d5210891cdb10858bc0a28ba7167909ab7c",
+    },
+    "8.2.0.53-10.2": {
+        "Linux-x86_64": "6ecbc98b3795e940ce0831ffb7cd2c0781830fdd6b1911f950bcaf6d569f807c"
+    },
+    # cuDNN 8.1.1
+    "8.1.1.33-11.2": {
+        "Linux-x86_64": "98a8784e92862f20018d20c281b30d4a0cd951f93694f6433ccf4ae9c502ba6a",
+        "Linux-ppc64le": "c3e535a5d633ad8f4d50be0b6f8efd084c6c6ed3525c07cbd89fc508b1d76c7a",
+        "Linux-aarch64": "4f7e4f5698539659d51f28dff0da11e5445a5ae58439af1d8a8e9f2d93535245",
+    },
+    "8.1.1.33-10.2": {
+        "Linux-x86_64": "2a4a7b99a6e9bfa690eb19bb41e49553f2a7a491a5b3abfcae900e166c5b6ebd"
+    },
+    # cuDNN 8.1.0
+    "8.1.0.77-11.2": {
+        "Linux-x86_64": "dbe82faf071d91ba9bcf00480146ad33f462482dfee56caf4479c1b8dabe3ecb",
+        "Linux-ppc64le": "0d3f8fa21959e9f94889841cc8445aecf41d2f3c557091b447313afb43034037",
+        "Linux-aarch64": "ba16ff486b68a8b50b69b32702612634954de529f39cfff68c12b8bfc1958499",
+    },
+    "8.1.0.77-10.2": {
+        "Linux-x86_64": "c5bc617d89198b0fbe485156446be15a08aee37f7aff41c797b120912f2b14b4"
+    },
+    # cuDNN 8.0.5
+    "8.0.5.39-11.1": {
+        "Linux-x86_64": "1d046bfa79399dabcc6f6cb1507918754439442ea0ca9e0fbecdd446f9b00cce",
+        "Linux-aarch64": "0c3542c51b42131247cd9f839d0ebefe4e02bb46d1716be1682cb2919278085a",
+    },
+    "8.0.5.39-11.0": {
+        "Linux-x86_64": "4e16ee7895deb4a8b1c194b812ba49586ef7d26902051401d3717511898a9b73",
+        "Linux-ppc64le": "05207a02c0b4f22464dbb0ee646693df4a70ae557640ba576ba8678c26393004",
+    },
+    "8.0.5.39-10.2": {
+        "Linux-x86_64": "21f84c05c67bf1ec859e77c38ccd5bf154964fa1c308f449959be4c356e382f3",
+        "Linux-ppc64le": "ce128ea090b05e36d00ffe921e45982ca10e8207e40cfc2e0067d0f62d9b36f9",
+    },
+    "8.0.5.39-10.1": {
+        "Linux-x86_64": "90908495298896b33aa95063a3471f93c36627d7ac01c17dc36d75c65eea4a00",
+        "Linux-ppc64le": "e43b10bb3932d5e7a598dcc726d16dc9938dd99dd319cd74b3420f3ed65fe5e0",
+    },
+    # cuDNN 8.0.4
+    "8.0.4.30-11.1": {
+        "Linux-x86_64": "8f4c662343afce5998ce963500fe3bb167e9a508c1a1a949d821a4b80fa9beab",
+        "Linux-ppc64le": "b4ddb51610cbae806017616698635a9914c3e1eb14259f3a39ee5c84e7106712",
+    },
+    "8.0.4.30-11.0": {
+        "Linux-x86_64": "38a81a28952e314e21577432b0bab68357ef9de7f6c8858f721f78df9ee60c35",
+        "Linux-ppc64le": "8da8ed689b1a348182ddd3f59b6758a502e11dc6708c33f96e3b4a40e033d2e1",
+    },
+    "8.0.4.30-10.2": {
+        "Linux-x86_64": "c12c69eb16698eacac40aa46b9ce399d4cd86efb6ff0c105142f8a28fcfb980e",
+        "Linux-ppc64le": "32a5b92f9e1ef2be90e10f220c4ab144ca59d215eb6a386e93597f447aa6507e",
+    },
+    "8.0.4.30-10.1": {
+        "Linux-x86_64": "eb4b888e61715168f57a0a0a21c281ada6856b728e5112618ed15f8637487715",
+        "Linux-ppc64le": "690811bbf04adef635f4a6f480575fc2a558c4a2c98c85c7090a3a8c60dacea9",
+    },
+    # cuDNN 8.0.3
+    "8.0.3.33-11.0": {
+        "Linux-x86_64": "8924bcc4f833734bdd0009050d110ad0c8419d3796010cf7bc515df654f6065a",
+        "Linux-ppc64le": "c2d0519831137b43d0eebe07522edb4ef5d62320e65e5d5fa840a9856f25923d",
+    },
+    "8.0.3.33-10.2": {
+        "Linux-x86_64": "b3d487c621e24b5711983b89bb8ad34f0378bdbf8a1a4b86eefaa23b19956dcc",
+        "Linux-ppc64le": "ff22c9c37af191c9104989d784427cde744cdde879bfebf3e4e55ca6a9634a11",
+    },
+    "8.0.3.33-10.1": {
+        "Linux-x86_64": "4752ac6aea4e4d2226061610d6843da6338ef75a93518aa9ce50d0f58df5fb07",
+        "Linux-ppc64le": "c546175f6ec86a11ee8fb9ab5526fa8d854322545769a87d35b1a505992f89c3",
+    },
+    # cuDNN 8.0.2
+    "8.0.2.39-11.0": {
+        "Linux-x86_64": "672f46288b8edd98f8d156a4f1ff518201ca6de0cff67915ceaa37f6d6d86345",
+        "Linux-ppc64le": "b7c1ce5b1191eb007ba3455ea5f497fdce293a646545d8a6ed93e9bb06d7f057",
+    },
+    "8.0.2.39-10.2": {
+        "Linux-x86_64": "c9cbe5c211360f3cfbc0fb104f0e9096b37e53f89392525679f049276b2f701f",
+        "Linux-ppc64le": "c32325ff84a8123491f2e58b3694885a9a672005bc21764b38874688c0e43262",
+    },
+    "8.0.2.39-10.1": {
+        "Linux-x86_64": "82148a68bd6bdaab93af5e05bb1842b8ccb3ab7de7bed41f609a7616c102213d",
+        "Linux-ppc64le": "8196ec4f031356317baeccefbc4f61c8fccb2cf0bdef0a6431438918ddf68fb9",
+    },
+    # cuDNN 8.0
+    "8.0.0.180-11.0": {
+        "Linux-x86_64": "9e75ea70280a77de815e0bdc85d08b67e081bc99a708b574092142344d2ba07e",
+        "Linux-ppc64le": "1229e94731bbca63ee7f5a239f4e1838a51a301d896f3097fbf7377d74704060",
+    },
+    "8.0.0.180-10.2": {
+        "Linux-x86_64": "0c87c12358ee2b99d57c2a8c7560e3bb93e54bb929f5f8bec4964a72a2bb261d",
+        "Linux-ppc64le": "59e4ad6db15fcc374976e8052fe39e3f30f34079710fb3c7751a64c853d9243f",
+    },
+    # cuDNN 7.6.5
+    "7.6.5.32-10.2": {
+        "Linux-x86_64": "600267f2caaed2fd58eb214ba669d8ea35f396a7d19b94822e6b36f9f7088c20",
+        "Linux-ppc64le": "7dc08b6ab9331bfd12207d4802c61db1ad7cace7395b67a6e7b16efa0335668b",
+    },
+    "7.6.5.32-10.1": {
+        "Linux-x86_64": "7eaec8039a2c30ab0bc758d303588767693def6bf49b22485a2c00bf2e136cb3",
+        "Darwin-x86_64": "8ecce28a5ed388a2b9b2d239e08d7c550f53b79288e6d9e5eb4c152bfc711aff",
+        "Linux-ppc64le": "97b2faf73eedfc128f2f5762784d21467a95b2d5ba719825419c058f427cbf56",
+    },
+    "7.6.5.32-10.0": {
+        "Linux-x86_64": "28355e395f0b2b93ac2c83b61360b35ba6cd0377e44e78be197b6b61b4b492ba",
+        "Darwin-x86_64": "6fa0b819374da49102e285ecf7fcb8879df4d0b3cc430cc8b781cdeb41009b47",
+        "Linux-ppc64le": "b1717f4570083bbfc6b8b59f280bae4e4197cc1cb50e9d873c05adf670084c5b",
+    },
+    "7.6.5.32-9.2": {
+        "Linux-x86_64": "a2a2c7a8ba7b16d323b651766ee37dcfdbc2b50d920f73f8fde85005424960e4",
+        "Linux-ppc64le": "a11f44f9a827b7e69f527a9d260f1637694ff7c1674a3e46bd9ec054a08f9a76",
+    },
+    "7.6.5.32-9.0": {
+        "Linux-x86_64": "bd0a4c0090d5b02feec3f195738968690cc2470b9bc6026e6fe8ff245cd261c8"
+    },
+    # cuDNN 7.6.4
+    "7.6.4.38-10.1": {
+        "Linux-x86_64": "32091d115c0373027418620a09ebec3658a6bc467d011de7cdd0eb07d644b099",
+        "Darwin-x86_64": "bfced062c3689ced2c1fb49c7d5052e6bc3da6974c1eb707e4dcf8cd209d4236",
+        "Linux-ppc64le": "f3615fea50986a4dfd05d7a0cf83396dfdceefa9c209e8bf9691e20a48e420ce",
+    },
+    "7.6.4.38-10.0": {
+        "Linux-x86_64": "417bb5daf51377037eb2f5c87649000ca1b9cec0acb16cfe07cb1d3e9a961dbf",
+        "Darwin-x86_64": "af01ab841caec25087776a6b8fc7782883da12e590e24825ad1031f9ae0ed4b1",
+        "Linux-ppc64le": "c1725ad6bd7d7741e080a1e6da4b62eac027a94ac55c606cce261e3f829400bb",
+    },
+    "7.6.4.38-9.2": {
+        "Linux-x86_64": "c79156531e641289b6a6952888b9637059ef30defd43c3cf82acf38d67f60a27",
+        "Linux-ppc64le": "98d8aae2dcd851558397a9a30b73242f257e1556be17c83650e63a0685969884",
+    },
+    "7.6.4.38-9.0": {
+        "Linux-x86_64": "8db78c3623c192d4f03f3087b41c32cb0baac95e13408b5d9dabe626cb4aab5d"
+    },
+    # cuDNN 7.6.3
+    "7.6.3.30-10.1": {
+        "Linux-x86_64": "352557346d8111e2f954c494be1a90207103d316b8777c33e62b3a7f7b708961",
+        "Linux-ppc64le": "f274735a8fc31923d3623b1c3d2b1d0d35bb176687077c6a4d4353c6b900d8ee",
+    },
+    # cuDNN 7.5.1
+    "7.5.1.10-10.1": {
+        "Linux-x86_64": "2c833f43c9147d9a25a20947a4c5a5f5c33b2443240fd767f63b330c482e68e0",
+        "Linux-ppc64le": "a9e23bc83c970daec20874ccd1d8d80b648adf15440ecd0164818b330b1e2663",
+    },
+    "7.5.1.10-10.0": {
+        "Linux-x86_64": "c0a4ec438920aa581dd567117b9c316745b4a451ac739b1e04939a3d8b229985",
+        "Linux-ppc64le": "d9205718da5fbab85433476f9ff61fcf4b889d216d6eea26753bbc24d115dd70",
+    },
+    # cuDNN 7.5.0
+    "7.5.0.56-10.1": {
+        "Linux-x86_64": "c31697d6b71afe62838ad2e57da3c3c9419c4e9f5635d14b683ebe63f904fbc8",
+        "Linux-ppc64le": "15415eb714ab86ab6c7531f2cac6474b5dafd989479b062776c670b190e43638",
+    },
+    "7.5.0.56-10.0": {
+        "Linux-x86_64": "701097882cb745d4683bb7ff6c33b8a35c7c81be31bac78f05bad130e7e0b781",
+        "Linux-ppc64le": "f0c1cbd9de553c8e2a3893915bd5fff57b30e368ef4c964d783b6a877869e93a",
+    },
+    # cuDNN 7.3.0
+    "7.3.0.29-9.0": {
+        "Linux-x86_64": "403f9043ff2c7b2c5967454872275d07bca11fd41dfc7b21995eadcad6dbe49b"
+    },
+    # cuDNN 7.2.1
+    "7.2.1.38-9.0": {
+        "Linux-x86_64": "cf007437b9ac6250ec63b89c25f248d2597fdd01369c80146567f78e75ce4e37"
+    },
+    # cuDNN 7.1.3
+    "7.1.3-9.1": {
+        "Linux-x86_64": "dd616d3794167ceb923d706bf73e8d6acdda770751492b921ee6827cdf190228",
+        "Linux-ppc64le": "e3b4837f711b98a52faacc872a68b332c833917ef3cf87c0108f1d01af9b2931",
+    },
+    # cuDNN 6.0
+    "6.0-8.0": {
+        "Linux-x86_64": "9b09110af48c9a4d7b6344eb4b3e344daa84987ed6177d5c44319732f3bb7f9c"
+    },
+    # cuDNN 5.1
+    "5.1-8.0": {
+        "Linux-x86_64": "c10719b36f2dd6e9ddc63e3189affaa1a94d7d027e63b71c3f64d449ab0645ce"
+    },
+}
+
+
+class Cudnn(Package):
+    """NVIDIA cuDNN is a GPU-accelerated library of primitives for deep
+    neural networks"""
+
+    homepage = "https://developer.nvidia.com/cudnn"
+
+    # Latest versions available at:
+    #     https://developer.nvidia.com/rdp/cudnn-download
+    # Archived versions available at:
+    #     https://developer.nvidia.com/rdp/cudnn-archive
+    # Note that download links don't work from command line,
+    # need to use modified URLs like in url_for_version.
+    maintainers("adamjstewart", "bvanessen")
+
+    skip_version_audit = ["platform=darwin", "platform=windows"]
+
+    license("MIT")
+
+    for ver, packages in _versions.items():
+        key = "{0}-{1}".format(platform.system(), platform.machine())
+        pkg = packages.get(key)
+        cudnn_ver, cuda_ver = ver.split("-")
+        long_ver = "{0}-{1}".format(cudnn_ver, cuda_ver)
+        if pkg:
+            version(long_ver, sha256=pkg)
+            # Add constraints matching CUDA version to cuDNN version
+            # cuDNN builds for CUDA 11.x are compatible with all CUDA 11.x:
+            # https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#fntarg_2
+            if Version(cuda_ver) >= Version("11"):
+                cuda_ver = Version(cuda_ver).up_to(1)
+            depends_on("cuda@{}".format(cuda_ver), when="@{}".format(long_ver))
+
+    def url_for_version(self, version):
+        # Get the system and machine arch for building the file path
+        sys = "{0}-{1}".format(platform.system(), platform.machine())
+        # Munge it to match Nvidia's naming scheme
+        sys_key = sys.lower()
+        if version < Version("8.3.1"):
+            sys_key = (
+                sys_key.replace("x86_64", "x64")
+                .replace("darwin", "osx")
+                .replace("aarch64", "aarch64sbsa")
+            )
+        elif version < Version("8.8.0"):
+            sys_key = sys_key.replace("aarch64", "sbsa")
+
+        if version >= Version("8.3.1"):
+            # NOTE: upload layout changed for 8.3.1, they include a 10.2
+            # artifact for cuda@10.2 x86_64, but the runtime is only supported
+            # for cuda@11.  See
+            # https://docs.nvidia.com/deeplearning/cudnn/release-notes/rel_8.html
+            # As such, hacking the `directory` to include the extra
+            # local_installers/11.5 is included as this may not happen again.
+            directory = version[:3]
+            ver = version[:4]
+            cuda = version[4:]
+            directory = "{0}/local_installers/{1}".format(directory, cuda)
+        elif version >= Version("7.2"):
+            directory = version[:3]
+            ver = version[:4]
+            cuda = version[4:]
+        elif version >= Version("7.1"):
+            directory = version[:3]
+            ver = version[:2]
+            cuda = version[3:]
+        elif version >= Version("7.0"):
+            directory = version[:3]
+            ver = version[0]
+            cuda = version[3:]
+        else:
+            directory = version[:2]
+            ver = version[:2]
+            cuda = version[2:]
+
+        # 8.8.0 changed the base url again
+        if version >= Version("8.8.0"):
+            url = "https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/{0}/cudnn-{0}-{1}_cuda{2}-archive.tar.xz"
+            return url.format(sys_key, ver, cuda.up_to(1))
+        # 8.5.0 removed minor from cuda version
+        elif version >= Version("8.5.0"):
+            url = "https://developer.download.nvidia.com/compute/redist/cudnn/v{0}/cudnn-{1}-{2}_cuda{3}-archive.tar.xz"
+            return url.format(directory, sys_key, ver, cuda.up_to(1))
+        # 8.3.1 switched to xzip tarballs and reordered url parts.
+        elif version >= Version("8.3.1"):
+            url = "https://developer.download.nvidia.com/compute/redist/cudnn/v{0}/cudnn-{1}-{2}_cuda{3}-archive.tar.xz"
+            return url.format(directory, sys_key, ver, cuda)
+        else:
+            url = "https://developer.download.nvidia.com/compute/redist/cudnn/v{0}/cudnn-{1}-{2}-v{3}.tgz"
+            return url.format(directory, cuda, sys_key, ver)
+
+    def setup_run_environment(self, env):
+        # Package is not compiled, and does not work unless LD_LIBRARY_PATH is set
+        env.prepend_path("LD_LIBRARY_PATH", self.prefix.lib)
+
+        if self.spec.satisfies("target=ppc64le: platform=linux"):
+            env.set("cuDNN_ROOT", os.path.join(self.prefix, "targets", "ppc64le-linux"))
+
+    def install(self, spec, prefix):
+        install_tree(".", prefix)
+
+        if spec.satisfies("target=ppc64le: platform=linux"):
+            target_lib = os.path.join(prefix, "targets", "ppc64le-linux", "lib")
+            if os.path.isdir(target_lib) and not os.path.isdir(prefix.lib):
+                symlink(target_lib, prefix.lib)
+            target_include = os.path.join(prefix, "targets", "ppc64le-linux", "include")
+            if os.path.isdir(target_include) and not os.path.isdir(prefix.include):
+                symlink(target_include, prefix.include)
--- a/packages/hxtorch/fix-multi-site-packages.patch
+++ b/packages/hxtorch/fix-multi-site-packages.patch
+diff --git a/src/hxtorch/wscript b/src/hxtorch/wscript
+index aaf670f..39322c8 100644
+--- a/hxtorch/wscript
+++ b/hxtorch/wscript
+
+@@ -45,13 +45,19 @@
+     )
+ 
+     site_packages = site.getsitepackages()
+-    assert isinstance(site_packages, list) and len(site_packages) == 1
+-    includes_torch = [os.path.join(x, 'torch/include') for x in site_packages]
+-    includes_torch_csrc_api = [os.path.join(x, 'torch/include/torch/csrc/api/include') for x in site_packages]
+    includes_torch = []
+    includes_torch_csrc_api = []
+    for x in site_packages:
+        torch_inc = os.path.join(x, 'torch/include')
+        if os.path.exists(torch_inc):
+            includes_torch.append(torch_inc)
+        torch_csrc_inc = os.path.join(x, 'torch/include/torch/csrc/api/include')
+        if os.path.exists(torch_csrc_inc):
+            includes_torch_csrc_api.append(torch_csrc_inc)
+     libpath_torch = [os.path.join(x, 'torch/lib') for x in site_packages]
+     libnames = []
+     # if torch isn't available via site-packages, try sys.path/PYTHONPATH
+-    if not os.path.exists(libpath_torch[0]):
+    if not any([os.path.exists(x) for x in libpath_torch]):
+         # find other possible paths
+         libpath_torch = [os.path.join(x, 'torch/lib') for x in sys.path if 'torch' in x]
+         # filter on existance of path
+
--- a/packages/hxtorch/package.py
+++ b/packages/hxtorch/package.py
@@ -96,6 +96,8 @@ class Hxtorch(build_brainscales.BuildBrainscales):

    patch("include-SparseTensorUtils.patch", when="@:8.0-a5")

+    patch("fix-multi-site-packages.patch", when="@:10.0-a1")
+
    def install_test(self):
        with working_dir('spack-test', create=True):
            old_pythonpath = os.environ.get('PYTHONPATH', '')

--- a/packages/jaxsnn/fix-multi-site-packages.patch
+++ b/packages/jaxsnn/fix-multi-site-packages.patch
+diff --git a/src/hxtorch/wscript b/src/hxtorch/wscript
+index aaf670f..39322c8 100644
+--- a/hxtorch/wscript
+++ b/hxtorch/wscript
+
+@@ -45,13 +45,19 @@
+     )
+ 
+     site_packages = site.getsitepackages()
+-    assert isinstance(site_packages, list) and len(site_packages) == 1
+-    includes_torch = [os.path.join(x, 'torch/include') for x in site_packages]
+-    includes_torch_csrc_api = [os.path.join(x, 'torch/include/torch/csrc/api/include') for x in site_packages]
+    includes_torch = []
+    includes_torch_csrc_api = []
+    for x in site_packages:
+        torch_inc = os.path.join(x, 'torch/include')
+        if os.path.exists(torch_inc):
+            includes_torch.append(torch_inc)
+        torch_csrc_inc = os.path.join(x, 'torch/include/torch/csrc/api/include')
+        if os.path.exists(torch_csrc_inc):
+            includes_torch_csrc_api.append(torch_csrc_inc)
+     libpath_torch = [os.path.join(x, 'torch/lib') for x in site_packages]
+     libnames = []
+     # if torch isn't available via site-packages, try sys.path/PYTHONPATH
+-    if not os.path.exists(libpath_torch[0]):
+    if not any([os.path.exists(x) for x in libpath_torch]):
+         # find other possible paths
+         libpath_torch = [os.path.join(x, 'torch/lib') for x in sys.path if 'torch' in x]
+         # filter on existance of path
+
--- a/packages/jaxsnn/newjax.patch
+++ b/packages/jaxsnn/newjax.patch
+From d12ff24ccb39f861067661b01973862e83552baf Mon Sep 17 00:00:00 2001
+From: Elias Arnold <elias.arnold@kip.uni-heidelberg.de>
+Date: Mon, 31 Mar 2025 15:13:03 +0200
+Subject: [PATCH] fix: tests for new jax
+
+Change-Id: I278454c7a51c0c15071a7ab8496a9655c52ff495
+---
+
+diff --git a/tests/sw/event/hardware/utils_test.py b/tests/sw/event/hardware/utils_test.py
+index ab73452..0753947 100644
+--- a/jaxsnn/tests/sw/event/hardware/utils_test.py
+++ b/jaxsnn/tests/sw/event/hardware/utils_test.py
+@@ -15,12 +15,12 @@
+         rng = random.PRNGKey(42)
+         with_noise = add_noise_batch(spikes, rng, std=1)
+         assert_array_equal(
+-            with_noise.idx, np.array([[0, 1, 2, 5, 3, 4, 6, 7, 8, 9]])
+            with_noise.idx, np.array([[0, 1, 2, 3, 4, 6, 5, 7, 8, 9]])
+         )
+ 
+         with_noise = add_noise_batch(spikes, rng, std=3)
+         assert_array_equal(
+-            with_noise.idx, np.array([[2, 1, 0, 5, 6, 7, 3, 4, 8, 9]])
+            with_noise.idx, np.array([[0, 6, 1, 2, 3, 4, 5, 7, 8, 9]])
+         )
+ 
+     def test_sort_batch(self):
+diff --git a/tests/sw/event/tasks/constant_test.py b/tests/sw/event/tasks/constant_test.py
+index be82deb..a7906af 100644
+--- a/jaxsnn/tests/sw/event/tasks/constant_test.py
+++ b/jaxsnn/tests/sw/event/tasks/constant_test.py
+@@ -52,7 +52,7 @@
+         )
+ 
+         # init weights
+-        rng = random.PRNGKey(42)
+        rng = random.PRNGKey(45)
+         weights = init_fn(rng, input_shape)
+ 
+         loss_fn = partial(
+
--- a/packages/jaxsnn/package.py
+++ b/packages/jaxsnn/package.py
@@ -46,6 +46,9 @@ class Jaxsnn(build_brainscales.BuildBrainscales):
    extends('python')

    patch("include-SparseTensorUtils.patch", when="@:8.0-a5")
+    patch("newjax.patch", when="@:10.0-a1 ^py-jax@0.5:")
+
+    patch("fix-multi-site-packages.patch", when="@:10.0-a1")

    def install_test(self):
        with working_dir('spack-test', create=True):

--- a/packages/nest/package.py
+++ b/packages/nest/package.py
@@ -75,6 +75,8 @@ class Nest(CMakePackage):
            description="Enable direct reading of connectivity from SONATA files")
    variant('boost',    default=True,
            description="Enable optimizations provided via Boost library algorithms and containers")
+    variant('jemalloc', default=True,
+            description="Pull in jemalloc as run-time dependency.")
    # TODO add variants for neurosim and music when these are in spack

    conflicts('~gsl', when='@:2.10.99',
@@ -99,6 +101,7 @@ class Nest(CMakePackage):
    depends_on('hdf5+cxx+mpi',      when='@3.4.99:+sonata+mpi', type=('build', 'run'))
    depends_on('hdf5+cxx~mpi',      when='@3.4.99:+sonata~mpi', type=('build', 'run'))
    depends_on('py-pandas',         when='@3.4.99:+sonata', type=('build', 'run'))
+    depends_on('jemalloc',          when='@3:+jemalloc', type=('run', 'test'))

    depends_on('py-nose',           when='@:2.99.99+python+testsuite', type='test')
    depends_on('py-pytest',         when='@3.0:+testsuite', type='test')

--- a/packages/py-anywidget/package.py
+++ b/packages/py-anywidget/package.py
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyAnywidget(PythonPackage):
+    """Custom jupyter widgets made easy"""
+
+    homepage = "https://github.com/manzt/anywidget"
+    pypi = "anywidget/anywidget-0.9.16.tar.gz"
+
+    version("0.9.13", sha256="c655455bf51f82182eb23c5947d37cc41f0b1ffacaf7e2b763147a2332cb3f07")
+    version("0.9.12", sha256="25855b2496dc6541356b6d26ca0c9f9525203bb7cf2817f84b93bfe3f53cf81e")
+    version("0.9.11", sha256="58dded8e86ec27ce28760c9457317663113d9af608947ee6a8d0ecb528b22cdc")
+    version("0.9.10", sha256="390a628240981c09813c7523279ddcab82ff4fd3287add5433b78b1369089068")
+    version("0.8.1", sha256="a7627770be455f89afd7d58faff926f45ef52b53257ae3c595177d5ff9b12fd1")
+    version("0.8.0", sha256="847a0fece58ea7a32d20dccd54a026dd3dd28f76daa6b4f0a74c253e5c7cfeec")
+
+    depends_on("py-hatchling", type="build")
+    depends_on("py-hatch-jupyter-builder", type="build")
+    depends_on("py-ipywidgets@7.6:", type=("build", "run"))
+    depends_on("py-typing-extensions@4.2:", type=("build", "run"))
+    depends_on("py-psygnal@0.8.1:", type=("build", "run"))
--- a/packages/py-biobb-gromacs/package.py
+++ b/packages/py-biobb-gromacs/package.py
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyBiobbGromacs(PythonPackage):
+    """Biobb_gromacs is the Biobb module collection to perform
+    molecular dynamics simulations using the GROMACS MD suite"""
+
+    pypi = "biobb_gromacs/biobb_gromacs-4.1.1.tar.gz"
+
+    maintainers("d-beltran")
+
+    # Versions
+    version("4.1.1", sha256="270cce747fc214471527438c8319bda0613be5b76da9f4684e6f138d1927d2f7")
+
+    # Dependencies
+    depends_on("py-setuptools", type="build")
+    depends_on("python@3.8:", type=("build", "run"))
+    depends_on("py-biobb-common@4.1.0", type=("build", "run"))
+    # begin EBRAINS(modified): biobb-gromacs checks for a `gmx` binary, with no suffix
+    depends_on("gromacs+nosuffix", type=("run"))
+    # end EBRAINS
--- a/packages/py-bluepyopt/package.py
+++ b/packages/py-bluepyopt/package.py
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+from spack.package import *
+
+
+class PyBluepyopt(PythonPackage):
+    """Bluebrain Python Optimisation Library"""
+
+    homepage = "https://github.com/BlueBrain/BluePyOpt"
+    pypi = "bluepyopt/bluepyopt-1.9.27.tar.gz"
+
+    license("LGPL-3.0-only")
+
+    # NOTE : while adding new release check pmi_rank.patch compatibility
+    version("1.14.18", sha256="23d6239294d944c8f9d4ea298091bcf243d236735844e1bcba60535a0f520ca8")
+    version("1.14.11", sha256="fe2830c36699a93d2ef9ddef316da42f9c57ca6654c92356eab973ee2298ebf7")
+    version("1.14.4", sha256="7567fd736053250ca06030f67ad93c607b100c2b98df8dc588c26b64cb3e171c")
+
+    # patch required to avoid hpe-mpi linked mechanism library
+    patch("pmi_rank.patch")
+
+    variant("scoop", default=False, description="Use BluePyOpt together with py-scoop")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy@1.6:", type=("build", "run"))
+    depends_on("py-pandas@0.18:", type=("build", "run"))
+    depends_on("py-deap@1.3.3:", type=("build", "run"))
+    depends_on("py-efel@2.13:", type=("build", "run"))
+    depends_on("py-ipyparallel", type=("build", "run"))
+    depends_on("py-pickleshare@0.7.3:", type=("build", "run"))
+    depends_on("py-jinja2@2.8:", type=("build", "run"))
+    depends_on("py-future", type=("build", "run"))
+    depends_on("py-pebble@4.6:", type=("build", "run"))
+    depends_on("py-scoop@0.7:", type=("build", "run"), when="+scoop")
+    depends_on("neuron@7.4:", type=("build", "run"), when="@:1.14.4")
+    depends_on("neuron@7.8:", type=("build", "run"), when="@1.14.11:")
+
+    def setup_run_environment(self, env):
+        env.unset("PMI_RANK")
+        env.set("NEURON_INIT_MPI", "0")
--- a/packages/py-bluepyopt/pmi_rank.patch
+++ b/packages/py-bluepyopt/pmi_rank.patch
+diff --git a/bluepyopt/ephys/simulators.py b/bluepyopt/ephys/simulators.py
+index e71ad8b..3c93237 100644
+--- a/bluepyopt/ephys/simulators.py
+++ b/bluepyopt/ephys/simulators.py
+@@ -89,6 +89,12 @@ class NrnSimulator(object):
+             NrnSimulator._nrn_disable_banner()
+             self.banner_disabled = True
+ 
+        # certain mpi libraries (hpe-mpt) use PMI_RANK env variable to initialize
+        # MPI before calling MPI_Init (which is undesirable). Unset this variable
+        # if exist to avoid issue with loading neuron and mechanism library.
+        if 'PMI_RANK' in os.environ:
+            os.environ.pop("PMI_RANK")
+
+         import neuron  # NOQA
+ 
+         return neuron
--- a/packages/py-ipycanvas/package.py
+++ b/packages/py-ipycanvas/package.py
@@ -24,6 +24,7 @@ class PyIpycanvas(PythonPackage):
    # begin EBRAINS (added)
    depends_on("python@3.6:", when="@0.10:", type=("build", "run"))
    depends_on("python@3.7:", when="@0.11:", type=("build", "run"))
+    depends_on('py-jupyter-core', type=("build", "run"))
    # end EBRAINS
    depends_on("py-setuptools@40.8:", type="build")
    depends_on("py-jupyter-packaging@0.7", type="build")

--- a/packages/py-ipydatawidgets/package.py
+++ b/packages/py-ipydatawidgets/package.py
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyIpydatawidgets(PythonPackage):
+    """A set of widgets to help facilitate reuse of large datasets across widgets"""
+
+    homepage = "https://github.com/vidartf/ipydatawidgets"
+    pypi = "ipydatawidgets/ipydatawidgets-4.3.5.tar.gz"
+
+    version("4.3.5", sha256="394f2489576587cfd755377a09a067f46cad22081965092021fd1abcbe7852a8")
+    version("4.3.4", sha256="124c0fc7b10e2d1ad5c20942f3e5a7e6c28cc8283f1e1bb7283a2d0ee55832d9")
+    version("4.3.3", sha256="4fb2ce693fb268cdae900374cfa1a91641e22d9514d1ec1e62da747050924f76")
+    version("4.3.2", sha256="2f2b997f6569d3ee1f4f7e35db0cb1da08c077b21a88f1c01c59f5b986a31aa6")
+    version("4.3.1", sha256="a934e51a2ad84380c63ff55ecf09bcd23d56e2c47c55c9c6f068cc91bdc1a379")
+    version("4.2.0", sha256="d0e4b58b59b508165e8562b8f5d1dbfcd739855847ec0477bd9185a5e9b7c5bc")
+
+    depends_on("py-setuptools@40.8:", type="build")
+    depends_on("py-wheel", type="build")
+    depends_on("py-jupyterlab@3", type="build")
+    depends_on("py-jupyter-packaging", type="build")
+    depends_on("yarn", type="build")
+
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-six", when="@:4.3.1", type=("build", "run"))
+    depends_on("py-traittypes@0.2:", type=("build", "run"))
+    depends_on("py-ipywidgets@7:", type=("build", "run"))
+    depends_on("py-jupyter-core", type=("build", "run"))
--- a/packages/py-ipyreact/package.py
+++ b/packages/py-ipyreact/package.py
+# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
+# Spack Project Developers. See the top-level COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+from spack.package import *
+
+
+class PyIpyreact(PythonPackage):
+    """React for ipywidgets that just works"""
+
+    homepage = "https://github.com/widgetti/ipyreact"
+    pypi = "ipyreact/ipyreact-0.5.0.tar.gz"
+
+    version("0.5.0", sha256="398b37c57abbf3d453a0fb4bb34d39956f2de212276de053630ad907eabde9e5")
+    version("0.4.2", sha256="a74b9f61176ca75c1c80ccfc46c35a7ad5591a30612d0e1e6fdbf91549fbf6a6")
+    version("0.4.1", sha256="80560311eb4946a793d1108d21c893f697f45af71df52afe4a3cddfa0a9fadd4")
+    version("0.4.0", sha256="e1900052a14c548ff4943f01c5eec09881c29c96845e70dcd0fe25b6c234d268")
+
+    depends_on("py-hatchling", type="build")
+    depends_on("py-hatch-jupyter-builder", type="build")
+    depends_on("py-ipywidgets@7:", type=("build", "run"))
+    depends_on("py-anywidget@0.2:", type=("build", "run"))
+    depends_on("py-jupyter-core", type=("build", "run"))
--- a/packages/py-jax/package.py
+++ b/packages/py-jax/package.py
+# Copyright Spack Project Developers. See COPYRIGHT file for details.
+#
+# SPDX-License-Identifier: (Apache-2.0 OR MIT)
+
+
+from spack.package import *
+
+
+class PyJax(PythonPackage):
+    """Differentiate, compile, and transform Numpy code.
+
+    JAX is a Python library for accelerator-oriented array computation and program transformation,
+    designed for high-performance numerical computing and large-scale machine learning.
+    """
+
+    homepage = "https://github.com/jax-ml/jax"
+    pypi = "jax/jax-0.4.27.tar.gz"
+
+    license("Apache-2.0")
+    maintainers("adamjstewart", "jonas-eschle")
+
+    version("0.5.2", sha256="2aef7d1912df329470c47ce8f2e6521c105e84aa620311494048c391235087c6")
+    version("0.5.1", sha256="c098f74846ee718165bbfa83521ae10cd52cf50b47f043f8b33a6cfd3c20ddfd")
+    version("0.5.0", sha256="49df70bf293a345a7fb519f71193506d37a024c4f850b358042eb32d502c81c8")
+    version("0.4.38", sha256="43bae65881628319e0a2148e8f81a202fbc2b8d048e35c7cb1df2416672fa4a8")
+    version("0.4.37", sha256="7774f3d9e23fe199c65589c680c5a5be87a183b89598421a632d8245222b637b")
+    version("0.4.36", sha256="088bff0575d01fc82682a9af4eb07433d60de7e5164686bd2cea3439492e608a")
+    version("0.4.35", sha256="c0c986993026b10bf6f607fecb7417377460254640766ce40f1fef3fd139c12e")
+    version("0.4.34", sha256="44196854f40c5f9cea3142824b9f1051f85afc3fcf7593ec5479fc8db01c58db")
+    version("0.4.33", sha256="f0d788692fc0179653066c9e1c64e57311b8c15a389837fd7baf328abefcbb92")
+    version("0.4.32", sha256="eb703909968da161894fb6135a931c5f3d2aab64fff7cba5fcb803ce6d968e08")
+    version("0.4.31", sha256="fd2d470643a0073d822737f0788f71391656af7e62cc5b2e7995ee390ceac287")
+    version("0.4.30", sha256="94d74b5b2db0d80672b61d83f1f63ebf99d2ab7398ec12b2ca0c9d1e97afe577")
+    version("0.4.29", sha256="12904571eaefddcdc8c3b8d4936482b783d5a216e99ef5adcd3522fdfb4fc186")
+    version("0.4.28", sha256="dcf0a44aff2e1713f0a2b369281cd5b79d8c18fc1018905c4125897cb06b37e9")
+    version("0.4.27", sha256="f3d7f19bdc0a17ccdb305086099a5a90c704f904d4272a70debe06ae6552998c")
+    version("0.4.26", sha256="2cce025d0a279ec630d550524749bc8efe25d2ff47240d2a7d4cfbc5090c5383")
+    version("0.4.25", sha256="a8ee189c782de2b7b2ffb64a8916da380b882a617e2769aa429b71d79747b982")
+    version("0.4.24", sha256="4a6b6fd026ddd22653c7fa2fac1904c3de2dbe845b61ede08af9a5cc709662ae")
+    version("0.4.23", sha256="2a229a5a758d1b803891b2eaed329723f6b15b4258b14dc0ccb1498c84963685")
+    version("0.4.22", sha256="801434dda6e14f82a45fff753969a33281ab22fb2a50fe801b651390321057ba")
+    version("0.4.21", sha256="c97fd0d2751d6e1eb15aa2052ff7cfdc129f8fafc2c14cd779720658926a587b")
+    version("0.4.20", sha256="ea96a763a8b1a9374639d1159ab4de163461d01cd022f67c34c09581b71ed2ac")
+    version("0.4.19", sha256="29f87f9a50964d3ca5eeb2973de3462f0e8b4eca6d46027894a0e9a903420601")
+    version("0.4.18", sha256="776cf33890100803e98f45f9af10aa727271c6993d4e766c069118733c928132")
+    version("0.4.17", sha256="d7508a69e87835f534cb07a2f21d79cc1cb8c4cfdcf7fb010927267ef7355f1d")
+    version("0.4.16", sha256="e2ca82c9bf973c2c1c01f5340a583692b31f277aa3abd0544229c1fe5fa44b02")
+    version("0.4.15", sha256="2aa123ccef591e355dea94a6e714b6559f8e1d6368a576a223f97d031ece0d15")
+    version("0.4.14", sha256="18fed3881f26e8b13c8cb46eeeea3dba9eb4d48e3714d8e8f2304dd6e237083d")
+    version("0.4.13", sha256="03bfe6749dfe647f16f15f6616638adae6c4a7ca7167c75c21961ecfd3a3baaa")
+    version("0.4.12", sha256="d2de9a2388ffe002f16506d3ad1cc6e34d7536b98948e49c7e05bbcfe8e57998")
+    version("0.4.11", sha256="8b1cd443b698339df8d8807578ee141e5b67e36125b3945b146f600177d60d79")
+    version("0.4.10", sha256="1bf0f2720f778f2937301a16a4d5cd3497f13a4d6c970c24a88918a81816a888")
+    version("0.4.9", sha256="1ed135cd08f48e4baf10f6eafdb4a4cdae781f9052b5838c09c91a9f4fa75f09")
+    version("0.4.8", sha256="08116481f7336db16c24812bfb5e6f9786915f4c2f6ff4028331fa69e7535202")
+    version("0.4.7", sha256="5e7002d74db25f97c99b979d4ba1233b1ef26e1597e5fc468ad11d1c8a9dc4f8")
+    version("0.4.6", sha256="d06ea8fba4ed315ec55110396058cb48c8edb2ab0b412f28c8a123beee9e58ab")
+    version("0.4.5", sha256="1633e56d34b18ddfa7d2a216ce214fa6fa712d36552532aaa71da416aede7268")
+    version("0.4.4", sha256="39b07e07343ed7c74492ee5e75db77456d3afdd038a322671f09fc748f6392cb")
+    version("0.4.3", sha256="d43f08f940aa30eb339965cfb3d6bee2296537b0dc2f0c65ccae3009279529ae")
+
+    depends_on("py-setuptools", type="build")
+
+    with default_args(type=("build", "run")):
+        # setup.py
+        depends_on("python@3.10:", when="@0.4.31:")
+        depends_on("python@3.9:", when="@0.4.14:")
+        depends_on("py-ml-dtypes@0.4:", when="@0.4.29,0.4.35:")
+        depends_on("py-ml-dtypes@0.2:", when="@0.4.14:")
+        depends_on("py-ml-dtypes@0.1:", when="@0.4.9:")
+        depends_on("py-ml-dtypes@0.0.3:", when="@0.4.7:")
+        depends_on("py-numpy@1.25:", when="@0.5:")
+        depends_on("py-numpy@1.24:", when="@0.4.31:")
+        depends_on("py-numpy@1.22:", when="@0.4.14:")
+        depends_on("py-numpy@1.21:", when="@0.4.7:")
+        depends_on("py-numpy@1.20:", when="@0.3:")
+        # https://github.com/google/jax/issues/19246
+        depends_on("py-numpy@:1", when="@:0.4.25")
+        depends_on("py-opt-einsum")
+        depends_on("py-scipy@1.11.1:", when="@0.5:")
+        depends_on("py-scipy@1.10:", when="@0.4.31:")
+        depends_on("py-scipy@1.9:", when="@0.4.19:")
+        depends_on("py-scipy@1.7:", when="@0.4.7:")
+        depends_on("py-scipy@1.5:", when="@0.3:")
+
+        # jax/_src/lib/__init__.py
+        # https://github.com/google/jax/commit/8be057de1f50756fe7522f7e98b2f30fad56f7e4
+        for v in [
+            # "0.5.0",
+            # "0.4.38",
+            # "0.4.37",
+            # "0.4.36",
+            # "0.4.35",
+            # "0.4.34",
+            # "0.4.33",
+            # "0.4.32",
+            "0.4.31",
+            "0.4.30",
+            "0.4.29",
+            "0.4.28",
+            "0.4.27",
+            "0.4.26",
+            "0.4.25",
+            "0.4.24",
+            "0.4.23",
+            "0.4.22",
+            "0.4.21",
+            "0.4.20",
+            "0.4.19",
+            "0.4.18",
+            "0.4.17",
+            "0.4.16",
+            "0.4.15",
+            "0.4.14",
+            "0.4.13",
+            "0.4.12",
+            "0.4.11",
+            "0.4.10",
+            "0.4.9",
+            "0.4.8",
+            "0.4.7",
+            "0.4.6",
+            "0.4.5",
+            "0.4.4",
+            "0.4.3",
+        ]:
+            depends_on(f"py-jaxlib@:{v}", when=f"@{v}")
+
+        # See _minimum_jaxlib_version in jax/version.py
+        # depends_on("py-jaxlib@0.5:", when="@0.5:")
+        # depends_on("py-jaxlib@0.4.38:", when="@0.4.38:")
+        # depends_on("py-jaxlib@0.4.36:", when="@0.4.36:")
+        # depends_on("py-jaxlib@0.4.35:", when="@0.4.35:")
+        # depends_on("py-jaxlib@0.4.34:", when="@0.4.34:")
+        # depends_on("py-jaxlib@0.4.33:", when="@0.4.33:")
+        # depends_on("py-jaxlib@0.4.32:", when="@0.4.32:")
+        depends_on("py-jaxlib@0.4.30:", when="@0.4.31:")
+        depends_on("py-jaxlib@0.4.27:", when="@0.4.28:")
+        depends_on("py-jaxlib@0.4.23:", when="@0.4.27:")
+        depends_on("py-jaxlib@0.4.20:", when="@0.4.25:")
+        depends_on("py-jaxlib@0.4.19:", when="@0.4.21:")
+        depends_on("py-jaxlib@0.4.14:", when="@0.4.15:")
+        depends_on("py-jaxlib@0.4.11:", when="@0.4.12:")
+        depends_on("py-jaxlib@0.4.7:", when="@0.4.8:")
+        depends_on("py-jaxlib@0.4.6:", when="@0.4.7:")
+        depends_on("py-jaxlib@0.4.4:", when="@0.4.5:")
+        depends_on("py-jaxlib@0.4.2:", when="@0.4.3:")
+        depends_on("py-jaxlib@0.4.1:", when="@0.4.2:")
+
+        # Historical dependencies
+        depends_on("py-importlib-metadata@4.6:", when="@0.4.11:0.4.30 ^python@:3.9")
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